## ----setup, message=FALSE-----------------------------------------------------
library(PubMatrixR)
library(knitr)
library(kableExtra)
library(dplyr)
library(pheatmap)
library(ggplot2)

## ----setup-live-flag, include = FALSE-----------------------------------------
# To render this vignette with real NCBI data instead of the offline
# fallback, set PUBMATRIX_LIVE_VIGNETTE=true (optionally with NCBI_API_KEY
# for a higher rate limit) before rendering, e.g.:
#
#   NCBI_API_KEY=your_api_key_here PUBMATRIX_LIVE_VIGNETTE=true \
#     Rscript -e 'pkgdown::build_site()'
#
# Left unset (the default, including in CI), both chunks below use the
# offline synthetic matrix and no network calls are made.
live <- identical(Sys.getenv("PUBMATRIX_LIVE_VIGNETTE"), "true")

ncbi_api_key <- Sys.getenv("NCBI_API_KEY", unset = "")
if (!nzchar(ncbi_api_key)) ncbi_api_key <- NULL

## ----gene_lists---------------------------------------------------------------
A <- c(
  "WNT1", "WNT2", "WNT2B", "WNT3", "WNT3A", "WNT4", "WNT5A", "WNT5B",
  "WNT6", "WNT7A", "WNT7B", "WNT8A", "WNT8B", "WNT9A", "WNT9B",
  "WNT10A", "WNT10B", "WNT11", "WNT16"
)

B <- c(
  "FZD1", "FZD2", "FZD3", "FZD4", "FZD5", "FZD6", "FZD7",
  "FZD8", "FZD9", "FZD10", "LRP5", "LRP6", "ROR1", "ROR2", "RYK"
)

## ----api_key_example, eval = FALSE--------------------------------------------
# result <- PubMatrix(
#   A = A,
#   B = B,
#   API.key = "your_api_key_here",
#   Database = "pubmed"
# )

## ----pubmatrix_analysis, eval = live------------------------------------------
# current_year <- as.integer(format(Sys.Date(), "%Y"))
# result <- PubMatrix(
#   A = A,
#   B = B,
#   API.key = ncbi_api_key,
#   Database = "pubmed",
#   daterange = c(1990, current_year),
#   outfile = "pubmatrix_result"
# )

## ----pubmatrix_analysis_offline, eval = !live---------------------------------
# Offline deterministic example used for vignette rendering/package checks.
result <- outer(seq_along(B), seq_along(A), function(i, j) {
  10 + (i * 5) + (j * 4) + ((i + j) %% 5) * 2 + ((i * j) %% 6)
})
result <- as.data.frame(result, check.names = FALSE)
colnames(result) <- A
rownames(result) <- B

## ----bar_plots, fig.width=10, fig.height=7, out.width="100%", dpi=150---------
# Create data frame for List A genes (rows) colored by List B genes (columns)
a_genes_data <- data.frame(
  gene = rownames(result),
  total_pubs = rowSums(result),
  stringsAsFactors = FALSE
)

# Add color coding based on max overlap with B genes
a_genes_data$max_b_gene <- apply(result, 1, function(x) colnames(result)[which.max(x)])
a_genes_data$max_overlap <- apply(result, 1, max)

# Create data frame for List B genes (columns) colored by List A genes (rows)
b_genes_data <- data.frame(
  gene = colnames(result),
  total_pubs = colSums(result),
  stringsAsFactors = FALSE
)

# Add color coding based on max overlap with A genes
b_genes_data$max_a_gene <- apply(result, 2, function(x) rownames(result)[which.max(x)])
b_genes_data$max_overlap <- apply(result, 2, max)

# Plot A genes colored by their strongest B gene partner
p1 <- ggplot(a_genes_data, aes(x = reorder(gene, total_pubs), y = total_pubs, fill = max_b_gene)) +
  geom_bar(stat = "identity") +
  coord_flip() +
  labs(
    title = "List A Genes by Publication Count",
    subtitle = "Colored by strongest List B gene partner",
    x = "Genes (List A)",
    y = "Total Publications",
    fill = "Strongest B Partner"
  ) +
  theme_minimal() +
  theme(legend.position = "bottom") +
  scale_fill_viridis_d()


# Plot B genes colored by their strongest A gene partner
p2 <- ggplot(b_genes_data, aes(x = reorder(gene, total_pubs), y = total_pubs, fill = max_a_gene)) +
  geom_bar(stat = "identity") +
  coord_flip() +
  labs(
    title = "List B Genes by Publication Count",
    subtitle = "Colored by strongest List A gene partner",
    x = "Genes (List B)",
    y = "Total Publications",
    fill = "Strongest A Partner"
  ) +
  theme_minimal() +
  theme(legend.position = "bottom") +
  scale_fill_viridis_d()


print(p1)
print(p2)

## ----results_table------------------------------------------------------------
kable(result,
  caption = "Co-occurrence Matrix: WNT Genes (Publication Counts)",
  align = "c",
  format = if (knitr::pandoc_to() == "html") "html" else "markdown"
) %>%
  kableExtra::kable_styling(
    bootstrap_options = c("striped", "hover", "condensed"),
    full_width = FALSE,
    position = "center"
  ) %>%
  kableExtra::add_header_above(c(" " = 1, "Wnt Genes" = length(A)))

## ----heatmap_with_numbers, fig.width=8, fig.height=6, out.width="100%", dpi=150----
plot_pubmatrix_heatmap(
  matrix = result,
  title = "WNT - Ligands v/s Receptors",
  show_numbers = TRUE
)

## ----heatmap_clean, fig.width=8, fig.height=6, out.width="100%", dpi=150------
pubmatrix_heatmap(matrix = result)

## ----system_info--------------------------------------------------------------
sessionInfo()